Narsis Kiani

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Articles

Article: NATURE MACHINE INTELLIGENCE. 2023;5(12):1437-1446

Reusability report: Learning the transcriptional grammar in single-cell RNA-sequencing data using transformers

Khan SA; Maillo A; Lagani V; Lehmann R; Kiani NA; Gomez-Cabrero D; Tegner J
Article: BREAST. 2023;70:18-24

Risk-adjusted benchmarking of long-term overall survival in patients with HER2-positive early-stage Breast cancer: A Swedish retrospective cohort study

Thurell J; Manouchehri N; Fredriksson I; Wilking U; Bergh J; Ryden L; Koppert LB; Karsten MM; Kiani NA; Hedayati E
Article: CANCER MEDICINE. 2023;12(9):10840-10850

Planning for return to work during the first year after breast cancer metastasis: A Swedish cohort study

Johnsson A; Kiani NA; Gernaat SAM; Wilking U; Shabo I; Hedayati E
Article: PLOS COMPUTATIONAL BIOLOGY. 2023;19(2):e1010811

LSD-induced increase of Ising temperature and algorithmic complexity of brain dynamics

Ruffini G; Damiani G; Lozano-Soldevilla D; Deco N; Rosas FEE; Kiani NAA; Ponce-Alvarez A; Kringelbach MLL; Carhart-Harris R; Deco G
Article: PLOS ONE. 2023;18(2):e0281315

scAEGAN: Unification of single-cell genomics data by adversarial learning of latent space correspondences

Khan SA; Lehmann R; Martinez-de-Morentin X; Maillo A; Lagani V; Kiani NA; Gomez-Cabrero D; Tegner J
Article: EUROPEAN JOURNAL OF CANCER CARE. 2022;31(5):e13626

Use of sickness benefits by patients with metastatic breast cancer-A Swedish cohort study

Altena R; Gernaat SAM; Wilking U; Kiani NA; Johnsson A; Hedayati E
Article: NUCLEIC ACIDS RESEARCH. 2020;48(19):10867-10876

MYC as a driver of stochastic chromatin networks: implications for the fitness of cancer cells

Sumida N; Sifakis EG; Kiani NA; Ronnegren AL; Scholz BA; Vestlund J; Gomez-Cabrero D; Tegner J; Gondor A; Ohlsson R
Article: PLASMONICS. 2020;15(2):417-426

Polarization Controlling of Multi Resonant Graphene-Based Microstrip Antenna

Jafari Chashmi M; Rezaei P; Kiani N
Article: OPTIK. 2020;200:163321

Y-shaped graphene-based antenna with switchable circular polarization

Chashmi MJ; Rezaei P; Kiani N
Article: FRONTIERS IN ARTIFICIAL INTELLIGENCE. 2020;3:567356

Algorithmic Probability-Guided Machine Learning on Non-Differentiable Spaces

Hernandez-Orozco S; Zenil H; Riedel J; Uccello A; Kiani NA; Tegner J
Article: FRONTIERS IN ONCOLOGY. 2020;10:51

Immunometabolic Network Interactions of the Kynurenine Pathway in Cutaneous Malignant Melanoma

Rad Pour S; Morikawa H; Kiani NA; Gomez-Cabrero D; Hayes A; Zheng X; Pernemalm M; Lehtio J; Mole DJ; Hansson J; Eriksson H; Tegner J
Article: ISCIENCE. 2019;19:1160-1172

An Algorithmic Information Calculus for Causal Discovery and Reprogramming Systems

Zenil H; Kiani NA; Marabita F; Deng Y; Elias S; Schmidt A; Ball G; Tegner J
Article: SCIENTIFIC REPORTS. 2019;9(1):12150

Exhaustion of CD4+T-cells mediated by the Kynurenine Pathway in Melanoma

Pour SR; Morikawa H; Kiani N; Yang M; Azimi A; Shafi G; Shang M; Baumgartner R; Ketelhuth DFJ; Kamleh MA; Wheelock CE; Lundqvist A; Hansson J; Tegner J
Article: JOURNAL OF LEUKOCYTE BIOLOGY. 2019;106(2):413-430

Phosphatase inhibitor PPP1R11 modulates resistance of human T cells toward Treg-mediated suppression of cytokine expression

Joshi RN; Fernandes SJ; Shang M-M; Kiani NA; Gomez-Cabrero D; Tegner J; Schmidt A
Article: NATURE COMMUNICATIONS. 2019;10(1):2674

Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen

Menden MP; Wang D; Mason MJ; Szalai B; Bulusu KC; Guan Y; Yu T; Kang J; Jeon M; Wolfinger R; Nguyen T; Zaslavskiy M; Jang IS; Ghazoui Z; Ahsen ME; Vogel R; Neto EC; Norman T; Tang EKY; Garnett MJ; Di Veroli GY; Fawell S; Stolovitzky G; Guinney J; Dry JR; Saez-Rodriguez J; Abante J; Abecassis BS; Aben N; Aghamirzaie D; Aittokallio T; Akhtari FS; Al-lazikani B; Alam T; Allam A; Allen C; de Almeida MP; Altarawy D; Alves V; Amadoz A; Anchang B; Antolin AA; Ash JR; Romeo Aznar V; Ba-alawi W; Bagheri M; Bajic V; Ball G; Ballester PJ; Baptista D; Bare C; Bateson M; Bender A; Bertrand D; Wijayawardena B; Boroevich KA; Bosdriesz E; Bougouffa S; Bounova G; Brouwer T; Bryant B; Calaza M; Calderone A; Calza S; Capuzzi S; Carbonell-Caballero J; Carlin D; Carter H; Castagnoli L; Celebi R; Cesareni G; Chang H; Chen G; Chen H; Chen H; Cheng L; Chernomoretz A; Chicco D; Cho K-H; Cho S; Choi D; Choi J; Choi K; Choi M; De Cock M; Coker E; Cortes-Ciriano I; Cserzo M; Cubuk C; Curtis C; Van Daele D; Dang CC; Dijkstra T; Dopazo J; Draghici S; Drosou A; Dumontier M; Ehrhart F; Eid F-E; ElHefnawi M; Elmarakeby H; van Engelen B; Engin HB; de Esch I; Evelo C; Falcao AO; Farag S; Fernandez-Lozano C; Fisch K; Flobak A; Fornari C; Foroushani ABK; Fotso DC; Fourches D; Friend S; Frigessi A; Gao F; Gao X; Gerold JM; Gestraud P; Ghosh S; Gillberg J; Godoy-Lorite A; Godynyuk L; Godzik A; Goldenberg A; Gomez-Cabrero D; Gonen M; de Graaf C; Gray H; Grechkin M; Guimera R; Guney E; Haibe-Kains B; Han Y; Hase T; He D; He L; Heath LS; Hellton KH; Helmer-Citterich M; Hidalgo MR; Hidru D; Hill SM; Hochreiter S; Hong S; Hovig E; Hsueh Y-C; Hu Z; Huang JK; Huang RS; Hunyady L; Hwang J; Hwang TH; Hwang W; Hwang Y; Isayev O; Walk OBD; Jack J; Jahandideh S; Ji J; Jo Y; Kamola PJ; Kanev GK; Karacosta L; Karimi M; Kaski S; Kazanov M; Khamis AM; Khan SA; Kiani NA; Kim A; Kim J; Kim J; Kim K; Kim K; Kim S; Kim Y; Kim Y; Kirk PDW; Kitano H; Klambauer G; Knowles D; Ko M; Kohn-Luque A; Kooistra AJ; Kuenemann MA; Kuiper M; Kurz C; Kwon M; van Laarhoven T; Laegreid A; Lederer S; Lee H; Lee J; Lee YW; Leppaho E; Lewis R; Li J; Li L; Liley J; Lim WK; Lin C; Liu Y; Lopez Y; Low J; Lysenko A; Machado D; Madhukar N; De Maeyer D; Malpartida AB; Mamitsuka H; Marabita F; Marchal K; Marttinen P; Mason D; Mazaheri A; Mehmood A; Mehreen A; Michaut M; Miller RA; Mitsopoulos C; Modos D; Van Moerbeke M; Moo K; Motsinger-Reif A; Movva R; Muraru S; Muratov E; Mushthofa M; Nagarajan N; Nakken S; Nath A; Neuvial P; Newton R; Ning Z; De Niz C; Oliva B; Olsen C; Palmeri A; Panesar B; Papadopoulos S; Park J; Park S; Park S; Pawitan Y; Peluso D; Pendyala S; Peng J; Perfetto L; Pirro S; Plevritis S; Politi R; Poon H; Porta E; Prellner I; Preuer K; Angel Pujana M; Ramnarine R; Reid JE; Reyal F; Richardson S; Ricketts C; Rieswijk L; Rocha M; Rodriguez-Gonzalvez C; Roell K; Rotroff D; de Ruiter JR; Rukawa P; Sadacca B; Safikhani Z; Safitri F; Sales-Pardo M; Sauer S; Schlichting M; Seoane JA; Serra J; Shang M-M; Sharma A; Sharma H; Shen Y; Shiga M; Shin M; Shkedy Z; Shopsowitz K; Sinai S; Skola D; Smirnov P; Soerensen IF; Soerensen P; Song J-H; Song SO; Soufan O; Spitzmueller A; Steipe B; Suphavilai C; Tamayo SP; Tamborero D; Tang J; Tanoli Z-U; Tarres-Deulofeu M; Tegner J; Thommesen L; Tonekaboni SAM; Tran H; De Troyer E; Truong A; Tsunoda T; Turu G; Tzeng G-Y; Verbeke L; Videla S; Vis D; Voronkov A; Votis K; Wang A; Wang H-QH; Wang P-W; Wang S; Wang W; Wang X; Wang X; Wennerberg K; Wernisch L; Wessels L; van Westen GJP; Westerman BA; White SR; Willighagen E; Wurdinger T; Xie L; Xie S; Xu H; Yadav B; Yau C; Yeerna H; Yin JW; Yu M; Yu M; Yun SJ; Zakharov A; Zamichos A; Zanin M; Zeng L; Zenil H; Zhang F; Zhang P; Zhang W; Zhao H; Zhao L; Zheng W; Zoufir A; Zucknick M
Article: ENTROPY. 2019;21(6):E560-560

The Thermodynamics of Network Coding, and an Algorithmic Refinement of the Principle of Maximum Entropy

Zenil H; Kiani NA; Tegner J
Article: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2019;116(19):9671-9676

MAPK pathway and B cells overactivation in multiple sclerosis revealed by phosphoproteomics and genomic analysis

Kotelnikova E; Kiani NA; Messinis D; Pertsovskaya I; Pliaka V; Bernardo-Faura M; Rinas M; Vila G; Zubizarreta I; Pulido-Valdeolivas I; Sakellaropoulos T; Faigle W; Silberberg G; Masso M; Stridh P; Behrens J; Olsson T; Martin R; Paul F; Alexopoulos LG; Saez-Rodriguez J; Tegner J; Villoslada P
Article: OPTIK. 2019;184:421-427

Reconfigurable graphene-based V-shaped dipole antenna: From quasi-isotropic to directional radiation pattern

Chashmi MJ; Rezaei P; Kiani N
Article: NATURE MACHINE INTELLIGENCE. 2019;1(1):58-66

Causal deconvolution by algorithmic generative models

Zenil H; Kiani NA; Zea AA; Tegner J
Article: ENTROPY. 2018;20(8):E605-605

A Decomposition Method for Global Evaluation of Shannon Entropy and Local Estimations of Algorithmic Complexity

Zenil H; Hernandez-Orozco S; Kiani NA; Soler-Toscano F; Rueda-Toicen A; Tegner J
Article: ROYAL SOCIETY OPEN SCIENCE. 2018;5(8):180399

Algorithmically probable mutations reproduce aspects of evolution, such as convergence rate, genetic memory and modularity

Hernandez-Orozco S; Kiani NA; Zenil H
Article: ENTROPY. 2018;20(7):E534-534

Symmetry and Correspondence of Algorithmic Complexity over Geometric, Spatial and Topological Representations

Zenil H; Kiani NA; Tegner J
Article: BMC BIOLOGY. 2018;16(1):47

Time-resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3

Schmidt A; Marabita F; Kiani NA; Gross CC; Johansson HJ; Elias S; Rautio S; Eriksson M; Fernandes SJ; Silberberg G; Ullah U; Bhatia U; Lahdesmaki H; Lehtio J; Gomez-Cabrero D; Wiendl H; Lahesmaa R; Tegner J
Article: JOURNAL OF TRANSLATIONAL MEDICINE. 2018;16(1):34

Network modules uncover mechanisms of skeletal muscle dysfunction in COPD patients

Tenyi A; Cano I; Marabita F; Kiani N; Kalko SG; Barreiro E; de Atauri P; Cascante M; Gomez-Cabrero D; Roca J
Article: BIOINFORMATICS. 2017;33(24):3964-3972

HiDi: an efficient reverse engineering schema for large-scale dynamic regulatory network reconstruction using adaptive differentiation

Deng Y; Zenil H; Tegner J; Kiani NA
Article: PLOS COMPUTATIONAL BIOLOGY. 2017;13(10):e1005757

Dynamics and heterogeneity of brain damage in multiple sclerosis

Kotelnikova E; Kiani NA; Abad E; Martinez-Lapiscina EH; Andorra M; Zubizarreta I; Pulido-Valdeolivas I; Pertsovskaya I; Alexopoulos LG; Olsson T; Martin R; Paul F; Tegner J; Garcia-Ojalvo J; Villoslada P
Article: MATHEMATICAL BIOSCIENCES. 2017;289:1-8

A minimal unified model of disease trajectories captures hallmarks of multiple sclerosis

Kannan V; Kiani NA; Piehl F; Tegner J
Article: PHYSICAL REVIEW E. 2017;96(1):012308

Low-algorithmic-complexity entropy-deceiving graphs

Zenil H; Kiani NA; Tegner J
Article: SCIENTIFIC REPORTS. 2016;6:26170

Conditional Disease Development extracted from Longitudinal Health Care Cohort Data using Layered Network Construction

Kannan V; Swartz F; Kiani NA; Silberberg G; Tsipras G; Gomez-Cabrero D; Alexanderson K; Tegner J
Article: MULTIPLE SCLEROSIS JOURNAL. 2015;21(2):138-146

Signaling networks in MS: A systems-based approach to developing new pharmacological therapies

Kotelnikova E; Bernardo-Faura M; Silberberg G; Kiani NA; Messinis D; Melas IN; Artigas L; Schwartz E; Mazo I; Masso M; Alexopoulos LG; Manuel Mas J; Olsson T; Tegner J; Martin R; Zamora A; Paul F; Saez-Rodriguez J; Villoslada P
Article: SOFT COMPUTING. 2014;18(12):2461-2469

Laplace transform formula on fuzzy nth-order derivative and its application in fuzzy ordinary differential equations

Ahmadi MB; Kiani NA; Mikaeilvand N
Article: JOURNAL OF TRANSLATIONAL MEDICINE. 2014;12(Suppl 2):S4

Systems Medicine: from molecular features and models to the clinic in COPD

Gomez-Cabrero D; Menche J; Cano I; Abugessaisa I; Huertas-Miguelanez M; Tenyi A; Marin de Mas I; Kiani NA; Marabita F; Falciani F; Burrowes K; Maier D; Wagner P; Selivanov V; Cascante M; Roca J; Barabasi A-L; Tegner J
Article: BMC BIOINFORMATICS. 2014;15(1):250

Dynamic probabilistic threshold networks to infer signaling pathways from time-course perturbation data

Kiani NA; Kaderali L
Article: ANNALS OF OPERATIONS RESEARCH. 2012;196(1):459-468

Resource allocation for performance improvement

Nasrabadi N; Dehnokhalaji A; Kiani NA; Korhonen PJ; Wallenius J
Article: BMC BIOINFORMATICS. 2011;12:485

Normalizing for individual cell population context in the analysis of high-content cellular screens

Knapp B; Rebhan I; Kumar A; Matula P; Kiani NA; Binder M; Erfle H; Rohr K; Eils R; Bartenschlager R; Kaderali L
Article: INTERNATIONAL JOURNAL OF UNCERTAINTY FUZZINESS AND KNOWLEDGE-BASED SYSTEMS. 2011;19(6):999-1012

DEGENERACY IN FUZZY LINEAR PROGRAMMING AND ITS APPLICATION

Sigarpich LA; Allahviranloo T; Lotfi FH; Kiani NA
Article: JOURNAL OF BIOLOGICAL CHEMISTRY. 2011;286(31):27278-27287

Molecular Mechanism of Signal Perception and Integration by the Innate Immune Sensor Retinoic Acid-inducible Gene-I (RIG-I)

Binder M; Eberle F; Seitz S; Muecke N; Hueber CM; Kiani N; Kaderali L; Lohmann V; Dalpke A; Bartenschlager R
Article: INFORMATION SCIENCES. 2009;179(8):1207-1215

Toward the existence and uniqueness of solutions of second-order fuzzy differential equations

Allahviranloo T; Kiani NA; Barkhordari M
Article: INFORMATION SCIENCES. 2009;179(7):956-966

Solving fuzzy differential equations by differential transformation method

Allahviranloo T; Kiani NA; Motamedi N
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Review: CARDIO-ONCOLOGY. 2021;7(1):20

Evidence-based prediction and prevention of cardiovascular morbidity in adults treated for cancer

Altena R; Hubbert L; Kiani NA; Wengstrom Y; Bergh J; Hedayati E
Review: ENTROPY. 2018;20(8):E551-551

A Review of Graph and Network Complexity from an Algorithmic Information Perspective

Zenil H; Kiani NA; Tegner J
Review: METHODS IN MOLECULAR BIOLOGY. 2018;1800:535-557

Predictive Systems Toxicology.

Kiani NA; Shang M-M; Zenil H; Tegner J
Corrigendum: SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY. 2016;60:168

Methods of information theory and algorithmic complexity for network biology (vol 51, pg 32, 2016)

Zenil H; Kiani NA; Tegner J
Review: PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES. 2016;374(2080):20160144

A perspective on bridging scales and design of models using low-dimensional manifolds and data-driven model inference

Tegner J; Zenil H; Kiani NA; Ball G; Gomez-Cabrero D
Review: SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY. 2016;51:44-52

Evaluating network inference methods in terms of their ability to preserve the topology and complexity of genetic networks

Kiani NA; Zenil H; Olczak J; Tegner J
Review: SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY. 2016;51:32-43

Methods of information theory and algorithmic complexity for network biology

Zenil H; Kiani NA; Tegner J
Review: CURRENT PHARMACEUTICAL DESIGN. 2016;22(46):6911-6917

Systems Toxicology: Systematic Approach to Predict Toxicity

Kiani NA; Shang M-M; Tegner J
Review: WORLD J VIROL. 2013;2(2):18-31

High-throughput RNA interference screens integrative analysis: Towards a comprehensive understanding of the virus-host interplay.

Amberkar S; Kiani NA; Bartenschlager R; Alvisi G; Kaderali L

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